Eternal Sonata takes place in a dream world which centers around famed piano composer Frédéric Chopin, who died at the age of 39 due to tuberculosis. The plot centers around the concept that as he slept on his sickbed in his final hours, Chopin dreamed of a fairy-tale land in which people with incurable diseases have great magical powers. The game frequently throws subtle allusions to the player that elements of the world are in fact, Chopin's dream, and could have their material forms influenced by Chopin's life.

The first six chapters of the game are also inspired and named for Chopin pieces with story elements related to the piece mentioned. For example, Chapter 2, "Revolution," is named for the Revolutionary Etude, and during the chapter, the player is introduced to Andantino, a rebel group. There are also segments in which Chopin's pieces are played along to a high-res photo slideshow accompanied by a history lesson on a part of Chopin's life when he wrote the corresponding piece. It should also be mentioned that almost every main character and locale in the game is named after a musical term, such as "Polka" or "Chorus Plains."

The story also focuses around a 14-year-old girl named Polka, who is apparently the victim of an incurable illness that grants her magical healing powers as a side-effect. She bears a strong resemblance to Chopin's younger sister who also died at 14, and her hometown of Tenuto may be an allusion to the town of Zelazowa Wola where Chopin was born.

Polka is selling floral powder for a living at the game's onset, a hand-made medicine from her hometown of Tenuto, for a living in the nearby city of Ritardando, but finds that her business has been completely lost to a new medicine called mineral powder. Apparently, mineral powder is a cheap medicine and the only good that is not taxed by the government, who, coincidentally, also manufactures and distributes the medicine which apparently works faster than floral powder.

After meeting Frederic (Chopin), who believes the world is his dream, the two decide to head to Forte City, where Count Waltz resides, and ask him to lower the tax on floral powder. On the way, however, they are assaulted by Fugue, a servant of Count Waltz, who nearly kills them and leaves them for dead.

It happens that two other people, Allegretto and Beat, two young orphans from Ritardando, are also heading to Forte to ask the Count to remove the tax from bread, which they have been forced to steal to help feed other orphans who live in the sewers under the city. The pair eventually meets Polka and Frederic in Agogo Forest, where one of the area's twin guardians, March, has given them shelter. Apparently, Polka had been saved by small creatures called Agogos that normally were shy around humans. One of them approaches Polka and glows upon doing so, a phenomenon that is unfamiliar to the forest's guardian.

Along the way, the four meet a goatherd named Viola, who is battling people that have been turned into mindless monsters due to overuse of mineral powder. It should also be mentioned that Fort Fermata, Forte's only line of defense and only entrance from way of Ritardando, is unmanned and filled with mineral powder-made monsters.

Upon reaching Forte Castle, the group is assaulted by Tuba, another of the Count's goons and are thrown into the castle dungeon. There, they meet Salsa, the other guardian of Agogo Forest, who claims that she was jailed because she would not reveal the secret of glowing agogos to Count Waltz. The glowing agogos would apparently increase the strength of the mineral powder a hundred-fold, allowing Forte's army to grow stronger and in rapidly growing numbers.

The party escapes through a secret passage used by Andantino, a rebel group that plans to overthrow the Count. Their leaders, Jazz, Claves and Falsetto, decide to join the group and work together against the Count, but before reaching the city again, they are encountered by Tuba yet again, who, upon defeat, commits suicide by destroying the bridge to Fermata and sending the party down into the river.

Separated from the others, Allegretto, Viola, Jazz, Claves and Falsetto decide to head to Andante, the rebel city. On the way, Allegretto warns Jazz that a spy may have infiltrated his ranks and for him to use caution. He initially believes the spy to be Falsetto, but Claves convinces him that evidence suggests that Falsetto is not the culprit. After Jazz departs, Claves is assassinated by Rondo, who works for Count Waltz, for betraying the Count by revealing her purpose. Before dying, she sends a carrier pigeon, initially used for correspondence with Forte, to Baroque. Claves had apparently fallen in love with Jazz and thus decided to protect him. Claves' death weighs heavily on Falsetto, who also loved Jazz, because now "he'll never get over her" and she wanders off to an unspecified location.

Meanwhile, Polka, Frederic, Beat and Salsa have found themselves saved by a Baroque ship, captained by Prince Crescendo, the leader of Baroque. While onboard, the ship is attacked by pirates led by Captain Dolce, and the party defeats her, though she re-appears as an optional boss three more times in the game.

Crescendo reveals to the group that he has been aiding Andantino, but, with the suggestion of his wife, Serenade, he has decided to stop supporting the rebels for fear of provoking Forte into all-out war. He asks the group to deliver this message to Jazz personally. After the group leaves, the Count receives Claves' last message: Serenade is a spy. However, the Prince believes that Serenade's feelings are true, and that she did what she did out of love for her home country.

Arriving in Agogo Forest, the group meets Fugue once again and defeats him. Afterwards, Agogos appear around Polka, all of them glowing. Rondo, in hiding, sees this, and leaves to report deliver this information to the Count.

Most of the group reunites later in Ritardando, though Allegretto soon leaves to go find Polka in Tenuto. He finds a stone on a beach identical to a keepsake that Polka has had since childhood, that came from her "true love." He gives it to her in Tenuto without knowledge of the keepsake, which Polka threw into the ocean. It becomes obvious that feelings have developed between the two, though neither bear the courage to express such emotions.

Upon return to Baroque, the group learn that Jazz has pleaded with the Count make a decision on the escalating situation with Forte. As he deliberates, the party is advised by a priest to seek out "the light" at nearby Aria Temple. Arriving there, the party finds that they have been cornered by Rondo, who plans to take Polka away. However, Falsetto returns to aid the party, and they defeat the assassin.

However, Crescendo and Serenade have left Baroque so they may surrender unconditionally to Forte to avoid the destruction of their homeland. The party uses the castle's warp device to reach to attempt to reach the two, but on the way, they meet a fortune teller who has met Polka before, though she does not remember her. She draws a fortune that portends "bad luck," and the group continues on.

After catching up to Crescendo and Sereande in Mount Rock, where mineral powder ingredients have been mined, the group is confronted by Count Waltz himself, and his servant, Legato. When Crescendo attempts to surrender, Waltz claims he does not desire Baroque, but simply "the girl," referring to Polka, and promises to treat her kindly. When she goes to Count Waltz in an effort to save her friends, the servant Legato takes a glowing agogo and adds it to a batch of mineral powder, confirming Waltz's suspicions on strengthening the powder.

When Waltz strikes Polka, the party attacks him and ultimately defeats him, leaving Legato cornered. He decides he "has no other choice," and drinks the enhanced mineral powder, transforming into a giant beast called Ruined Body that is apparently so powerful that it is able to tear a hole through time and space.

The group follows Legato to the Elegy of the Moon, where the souls of people who used mineral powder have come to rest, unable to reach the afterlife. After conquering Xylophone Tower, a trial for those who wish to proceed, they reach Double Reed Tower and confront the transformed Legato.

After defeating Legato, the group reaches the end of the earth, where Frederic confronts them, saying that the entire world is his dream, and that upon reaching Death, one must face their very own soul before moving to the afterlife. The party faces Chopin in the game's finale, and upon defeating him, he thanks them, as his soul is now free to move on the afterlife.

Polka then approaches a cliff and tells the party that Death has always been her fate, that her mother has prepared her for this, and that her light would illuminate the darkness of the world upon her jump into the unknown. She leaps, leaving Allegretto mortified and their feelings for one another apparently unrealized. Then, Chopin's eyes open and he realizes that the world is not his dream, after all.

However, after a Staff Roll for the sound team and voice cast, a cinematic occurs that shows Polka's young self hovering down into her mother's arms. Chopin is proclaimed dead at approximately two o'clock in the morning afterwards. As the game's second opening cinematic occurs again, the player hears Chopin claim that Polka should be free to live her life and not be left to a fate of death. The young Polka then tells her mother that someone is calling her, someone "whose light matches (her) astra" and she leaves with her mother's blessing.

Rising back out of the abyss, surrounded by glowing Agogos, she sets foot on the ground, which turns into a field of flowers, and embraces Allegretto as they run into each other's arms.

Back in the "real" world, Chopin's soul rises from his body and approaches the piano and begins to play. As the melody ensues, a woman who has been by Chopin's side through his ordeal begins to sing along with his posthumous performance. Though the girl is not named, she could be assumed (and is hinted earlier in the game) to be Konstancja Gładkowska, his first love and the woman who inspired Chopin to put voice into his works.